Photobiomodulation therapy (PBM) has shown positive effects on stem cell differentiation in monolayer cell culture model, but little is known about its effect on three-dimensional (3-D) agarose gel culture. This study evaluated the PBM effect of human dental pulp stem cells (hDPSCs) differentiation and phosphatase alkaline activity (ALP) using an agarose 3-D model under different nutritional conditions. hDPSCs were characterized and seeded on a 0.3% agarose gel layer with different media (osteogenic, adipogenic, chondrogenic) and were assigned into four groups: control 10% fetal bovine serum (FBS), control 5% FBS, PBM 10% FBS, and PBM 5% FBS. Irradiation was performed with continuous-wave InGaAlP laser, 660 nm, 100 mW, 3,3 J / cm2, spot size 0.3 cm2, 10 s of exposure time, and 1 J of energy per point with 6-h interval between sessions. All groups were evaluated at 7 and 14 days. ALP assay was performed to analyze the deposition of mineralized tissue. At 7 days, PBM 5% FBS group presented better stimulation in osteogenic and adipogenic differentiation compared with control. After 14 days, hDPSCs cultured in 3-D exhibited osteogenic, adipogenic, and chondrogenic differentiation; furthermore, compared to control, PBM significantly stimulated all differentiation processes (p < 0.05). It can be concluded that hDPSCs cultured in 3-D agarose associated to PBM could be a promising tool for tissue engineering applications.